QC

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2024-05-09, 10:07 EDT based on data in:

/vf/users/DCEG_Trios/novaseq_benchmark/TriosCompass_v2/output/collectmultiplemetrics
/vf/users/DCEG_Trios/novaseq_benchmark/TriosCompass_v2/output/collectwgsmetrics
/vf/users/DCEG_Trios/novaseq_benchmark/TriosCompass_v2/output/fastp
/vf/users/DCEG_Trios/novaseq_benchmark/TriosCompass_v2/output/fastqc
/vf/users/DCEG_Trios/novaseq_benchmark/TriosCompass_v2/output/fastq_screen
/vf/users/DCEG_Trios/novaseq_benchmark/TriosCompass_v2/output/gatk_markdup
/vf/users/DCEG_Trios/novaseq_benchmark/TriosCompass_v2/output/dragen_gvcf

General Statistics

Showing ²⁸/₂₈ rows and ¹⁶/₃₈ columns.

Sample Name	M Input reads	Paired	QC-fail	Map	Unmap	Dup	Uniq map	Prop pair	Discord	Diff chr, MQ⩾10	Med IS	Q30	M Alignments	Sec'ry	Variants	Multiallelic	SNP	Indel	Ti/Tv	Het/Hom	Sex	Depth BED	Depth WGS	% GC	Insert Size	Mean Insert Size	Duplication	M Reads	Median Coverage	Mean Coverage	SD Coverage	Bases ≥ 30X	% Dups	% GC	Average Read Length	Median Read Length	% Failed	M Seqs
SC501095	2555.0 M	100.0%	0.00%	96.2%	3.8%	4.5%	91.7%	94.0%	1.22%	0.85%	332	90.4%	2467.2 M	0.00%	4849223	1.9%	80.4%	18.5%	2.0	1.5	XY	107.13 x	104.10 x	41%	346 bp	349 bp	4.3%		89.0X	81.9X	28.4X	93%
SC501095_B22CHLTLT3.R1																																	17.6%	40%	144 bp	151 bp	9%	1118.0 M
SC501095_B22CHLTLT3.R2																																	18.7%	40%	144 bp	151 bp	9%	1118.0 M
SC501096	2380.0 M	100.0%	0.00%	96.6%	3.4%	4.4%	92.2%	94.3%	1.30%	0.92%	369	89.0%	2307.7 M	0.00%	4904207	1.9%	80.4%	19.0%	2.0	1.6	XX	103.24 x	100.34 x	41%	384 bp	380 bp	4.0%		86.0X	80.2X	26.8X	93%
SC501096_B22CHLTLT3.R1																																	16.7%	40%	146 bp	151 bp	9%	1026.9 M
SC501096_B22CHLTLT3.R2																																	16.4%	40%	146 bp	151 bp	9%	1026.9 M
SC501105	2617.6 M	100.0%	0.00%	96.6%	3.4%	7.3%	89.4%	94.7%	1.05%	0.74%	302	90.6%	2537.8 M	0.00%	4885301	1.9%	80.4%	19.1%	2.0	1.6	XX	106.41 x	103.41 x	41%	324 bp	332 bp	7.0%		86.0X	80.6X	26.8X	93%
SC501105_B22CHLTLT3.R1																																	18.1%	40%	143 bp	151 bp	9%	1150.9 M
SC501105_B22CHLTLT3.R2																																	19.4%	40%	143 bp	151 bp	9%	1150.9 M
SC501108	2465.7 M	100.0%	0.00%	96.5%	3.5%	6.8%	89.7%	94.1%	1.32%	0.82%	380	88.3%	2386.9 M	0.00%	4867227	1.9%	80.5%	18.5%	2.0	1.6	XY	102.28 x	99.47 x	41%	376 bp	379 bp	6.2%		83.0X	77.0X	26.9X	93%
SC501108_B22CHLTLT3.R1																																	18.5%	40%	146 bp	151 bp	9%	1044.0 M
SC501108_B22CHLTLT3.R2																																	18.8%	40%	146 bp	151 bp	9%	1044.0 M
SC501110	2223.9 M	100.0%	0.00%	96.8%	3.2%	8.3%	88.5%	94.4%	1.40%	0.95%	347	90.2%	2159.4 M	0.00%	4884094	1.9%	80.4%	19.1%	2.0	1.6	XX	91.51 x	88.91 x	41%	362 bp	364 bp	7.8%		76.0X	71.4X	24.1X	92%
SC501110_B22CHLTLT3.R1																																	16.7%	40%	146 bp	151 bp	9%	974.8 M
SC501110_B22CHLTLT3.R2																																	16.6%	40%	146 bp	151 bp	18%	974.8 M
SC501111	2514.8 M	100.0%	0.00%	96.5%	3.5%	11.9%	84.5%	93.9%	1.50%	1.06%	385	90.1%	2433.9 M	0.00%	4844316	1.9%	80.4%	18.5%	2.0	1.6	XY	98.72 x	95.98 x	41%	386 bp	383 bp	11.2%		85.0X	78.6X	27.2X	93%
SC501111_B22CHLTLT3.R1																																	20.6%	40%	146 bp	151 bp	9%	1096.7 M
SC501111_B22CHLTLT3.R2																																	20.5%	40%	146 bp	151 bp	9%	1096.7 M
SD162355	2694.6 M	100.0%	0.00%	96.3%	3.7%	10.4%	85.9%	93.8%	1.57%	1.21%	326	91.7%	2606.5 M	0.00%	4896047	1.9%	80.4%	18.5%	2.0	1.6	XY	104.90 x	102.13 x	41%	327 bp	335 bp	10.1%		87.0X	81.0X	28.3X	93%
SD162355_A22FKHJLT3.R1																																	21.0%	41%	144 bp	151 bp	18%	1196.4 M
SD162355_A22FKHJLT3.R2																																	22.4%	41%	144 bp	151 bp	9%	1196.4 M
SD162357	2583.1 M	100.0%	0.00%	96.6%	3.4%	18.1%	78.5%	94.2%	1.43%	1.08%	390	92.1%	2503.2 M	0.00%	4877362	1.9%	80.4%	18.6%	2.0	1.6	XY	93.66 x	91.37 x	42%	380 bp	381 bp	17.8%		82.0X	76.3X	26.9X	93%
SD162357_A22FKHJLT3.R1																																	23.3%	41%	147 bp	151 bp	9%	1157.1 M
SD162357_A22FKHJLT3.R2																																	24.5%	41%	147 bp	151 bp	9%	1157.1 M
SD162359	2751.1 M	100.0%	0.00%	96.8%	3.2%	9.6%	87.1%	94.8%	1.11%	0.83%	296	92.5%	2670.8 M	0.00%	4946727	2.0%	80.5%	19.0%	2.0	1.6	XX	108.75 x	106.05 x	42%	320 bp	329 bp	9.5%		90.0X	84.7X	28.0X	93%
SD162359_A22FKHJLT3.R1																																	19.6%	41%	143 bp	151 bp	9%	1240.9 M
SD162359_A22FKHJLT3.R2																																	21.0%	41%	143 bp	151 bp	9%	1240.9 M
quality_yield																												2481.7 M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table

Sort	Group	Column	Description	ID	Scale
\|\|	DRAGEN: Mapping	M Input reads	Total number of input reads for this sample (or total number of reads in all input read groups combined), millions	`Total input reads`	read_count
\|\|	DRAGEN: Mapping	Paired	% of reads with a mate sequenced	`Reads with mate sequenced pct`	None
\|\|	DRAGEN: Mapping	QC-fail	% of reads not passing platform/vendor quality checks (SAM flag 0x200)	`QC-failed reads pct`	None
\|\|	DRAGEN: Mapping	Map	% of mapped reads	`Mapped reads pct`	None
\|\|	DRAGEN: Mapping	Unmap	% of unmapped reads	`Unmapped reads pct`	None
\|\|	DRAGEN: Mapping	Dup	% of duplicate marked reads as a result of the --enable-duplicatemarking option being used	`Number of duplicate marked reads pct`	None
\|\|	DRAGEN: Mapping	Uniq map	% of unique & mapped reads (mapped reads minus duplicate marked reads)	`Number of unique & mapped reads (excl. duplicate marked reads) pct`	None
\|\|	DRAGEN: Mapping	Prop pair	% of properly paired reads (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`Properly paired reads pct`	None
\|\|	DRAGEN: Mapping	Discord	% of discordant reads: paired reads minus properly paired reads	`Not properly paired reads (discordant) pct`	None
\|\|	DRAGEN: Mapping	Diff chr, MQ⩾10	% of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome	`Paired reads mapped to different chromosomes (MAPQ>=10) pct`	None
\|\|	DRAGEN: Mapping	Med IS	Median insert size	`Insert length: median`	None
\|\|	DRAGEN: Mapping	Q30	% of raw bases with BQ >= 30	`Q30 bases pct`	None
\|\|	DRAGEN: Mapping	M Alignments	Total number of alignments with MQ > 0, millions	`Total alignments`	read_count
\|\|	DRAGEN: Mapping	Sec'ry	% of secondary alignments. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`Secondary alignments pct`	None
\|\|	DRAGEN: Variant calling	Variants	Total number of variants (SNPs + MNPs + INDELS).	`Total`	None
\|\|	DRAGEN: Variant calling	Multiallelic	% of sites in the VCF that contain three or more observed alleles. The reference is counted as one, therefore allowing for two or more variant alleles	`Multiallelic pct`	None
\|\|	DRAGEN: Variant calling	SNP	% of SNPs in the variant set. A variant is counted as an SNP when the reference, allele 1, and allele2 are all length 1	`SNPs pct`	None
\|\|	DRAGEN: Variant calling	Indel	% of insetions and deletions in the variant set.	`Indels pct`	None
\|\|	DRAGEN: Variant calling	Ti/Tv	Ti/Tv ratio: ratio of transitions to transitions.	`Ti/Tv ratio`	None
\|\|	DRAGEN: Variant calling	Het/Hom	Heterozygous/ homozygous ratio	`Het/Hom ratio`	None
\|\|	DRAGEN: Ploidy estimation	Sex	Sex chromosome ploidy estimation (XX, XY, X0, 00, etc.)	`Ploidy estimation`	None
\|\|	DRAGEN: Coverage	Depth BED	Coverage depth over target region: number of uniquely mapped bases to target region divided by the number of sites in target region.	`target bed average alignment coverage over target region`	None
\|\|	DRAGEN: Coverage	Depth WGS	Coverage depth over genome: number of uniquely mapped bases to genome divided by the number of sites in genome.	`wgs average alignment coverage over genome`	None
\|\|	DRAGEN-FastQC: FastQC	% GC	Average % GC Content	`avg_gc_content_percent`	None
\|\|	Picard: InsertSizeMetrics	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	Picard: InsertSizeMetrics	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None
\|\|	Picard: Mark Duplicates	Duplication	Mark Duplicates - Percent Duplication	`PERCENT_DUPLICATION`	None
\|\|	Picard: QualityYieldMetrics	M Reads	The total number of reads in the input file (millions)	`TOTAL_READS`	read_count
\|\|	Picard: WgsMetrics	Median Coverage	The median coverage in bases of the genome territory, after all filters are applied.	`MEDIAN_COVERAGE`	None
\|\|	Picard: WgsMetrics	Mean Coverage	The mean coverage in bases of the genome territory, after all filters are applied.	`MEAN_COVERAGE`	None
\|\|	Picard: WgsMetrics	SD Coverage	The standard deviation coverage in bases of the genome territory, after all filters are applied.	`SD_COVERAGE`	None
\|\|	Picard: WgsMetrics	Bases ≥ 30X	Percent of target bases with coverage ≥ 30X	`PCT_30X`	None
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Average Read Length	Average Read Length (bp)	`avg_sequence_length`	None
\|\|	FastQC	Median Read Length	Median Read Length (bp)	`median_sequence_length`	None
\|\|	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

DRAGEN

DRAGEN is a Bio-IT Platform that provides ultra-rapid secondary analysis of sequencing data using field-programmable gate array technology (FPGA).

Mapping metrics

Mapping metrics, similar to the metrics computed by the samtools-stats command. Shown on per read group level. To see per-sample level metrics, refer to the general stats table.

Showing ⁹/₉ rows and ¹²/₇₁ columns.

Sample Name	Input reads	M Input reads	Paired	M Paired	Single	QC-fail	Map	M Map	Map R1	M Map R1	Map R2	M Map R2	Unmap	M Unmap	MQ⩾40	M MQ⩾40	Dup	M Dup	Uniq	Uniq map	M Uniq map	Self & mate map	M Self & mate map	Prop pair	M Prop pair	Discord	M Discord	Singleton	M Singleton	Diff chrom	M Diff chrom	Diff chr, MQ⩾10	M Diff chr, MQ⩾10	Reads with indel R1	M Reads with indel R1	Reads with indel R2	M Reads with indel R2	Read len	Avg IS	Med IS	IS std	Mb Input bases	Mb Input bases R1	Mb Input bases R2	Mapped bases R1	Mb Mapped bases R1	Mapped bases R2	Mb Mapped bases R2	Soft-clip bases R1	Mb Soft-clip bases R1	Soft-clip bases R2	MM bases R1	Mb MM bases R1	MM bases R2	MM bases R1 excl indels	Mb MM bases R1 excl indels	MM bases R2 excl indels	Q30	Mb Q30	Q30 R1	Mb Q30 R1	Q30 R2	Mb Q30 R2	Q30 excl dup & clipped	Mb Q30 excl dup & clipped	M Alignments	Sec'ry	M Suppl'ry
SC501095	100.0%	2555.0 M	100.0%	2555.0 M	0.0%	0.00%	96.2%	2458.4 M	96.8%	1237.3 M	95.6%	1221.1 M	3.8%	96.6 M	88.0%	2247.7 M	4.5%	115.0 M	95.5%	91.7%	2343.4 M	95.3%	2434.3 M	94.0%	2403.0 M	1.22%	31.23 M	0.94%	24.11 M	1.11%	27.02 M	0.85%	20.73 M	2.9%	35.5 M	2.7%	32.6 M	143.1	338.1	332	171.9	365659.5 Mb	182671.0 Mb	182988.5 Mb	48.5%	177315.7 Mb	47.8%	174966.2 Mb	0.8%	1370.6 Mb	1.2%	0.6%	1028.6 Mb	0.7%	0.5%	913.6 Mb	0.6%	90.4%	330405.2 Mb	91.7%	167434.4 Mb	89.1%	162970.9 Mb	86.4%	315769.0 Mb	2467.2 M	0.00%	8.77 M
SC501096	100.0%	2380.0 M	100.0%	2380.0 M	0.0%	0.00%	96.6%	2300.1 M	97.4%	1159.5 M	95.8%	1140.6 M	3.4%	79.9 M	89.1%	2121.5 M	4.4%	104.5 M	95.6%	92.2%	2195.6 M	95.6%	2274.7 M	94.3%	2243.7 M	1.30%	31.04 M	1.07%	25.41 M	1.16%	26.49 M	0.92%	20.84 M	3.0%	34.2 M	2.7%	31.3 M	146.3	367.5	369	163.6	348283.3 Mb	174049.5 Mb	174233.8 Mb	48.7%	169624.6 Mb	47.9%	166894.4 Mb	0.8%	1311.5 Mb	1.3%	0.7%	1114.5 Mb	0.8%	0.6%	1001.5 Mb	0.7%	89.0%	309943.9 Mb	90.5%	157533.0 Mb	87.5%	152410.9 Mb	85.2%	296650.9 Mb	2307.7 M	0.00%	7.62 M
SC501105	100.0%	2617.6 M	100.0%	2617.6 M	0.0%	0.00%	96.6%	2529.7 M	97.3%	1272.9 M	96.0%	1256.8 M	3.4%	87.9 M	88.7%	2320.4 M	7.3%	190.1 M	92.7%	89.4%	2339.6 M	95.8%	2506.9 M	94.7%	2479.4 M	1.05%	27.49 M	0.87%	22.83 M	0.95%	23.84 M	0.74%	18.60 M	2.8%	36.2 M	2.6%	33.3 M	142.2	313.0	302	165.2	372355.1 Mb	185951.5 Mb	186403.6 Mb	48.6%	181086.1 Mb	48.0%	178802.3 Mb	0.7%	1295.9 Mb	1.2%	0.6%	1026.0 Mb	0.7%	0.5%	907.8 Mb	0.6%	90.6%	337188.1 Mb	91.8%	170732.8 Mb	89.3%	166455.3 Mb	84.1%	313136.9 Mb	2537.8 M	0.00%	8.08 M
SC501108	100.0%	2465.7 M	100.0%	2465.7 M	0.0%	0.00%	96.5%	2379.4 M	97.3%	1199.4 M	95.7%	1180.0 M	3.5%	86.4 M	88.2%	2174.1 M	6.8%	167.5 M	93.2%	89.7%	2211.9 M	95.4%	2352.2 M	94.1%	2319.7 M	1.32%	32.47 M	1.10%	27.15 M	1.17%	27.47 M	0.82%	19.19 M	3.0%	36.0 M	2.8%	33.0 M	145.3	385.3	380	186.3	358404.0 Mb	179019.9 Mb	179384.1 Mb	48.7%	174377.1 Mb	47.9%	171567.0 Mb	0.8%	1391.0 Mb	1.5%	0.7%	1147.4 Mb	0.9%	0.6%	1025.5 Mb	0.8%	88.3%	316617.8 Mb	91.0%	162813.4 Mb	85.7%	153804.4 Mb	82.6%	295865.8 Mb	2386.9 M	0.00%	7.51 M
SC501110	100.0%	2223.9 M	100.0%	2223.9 M	0.0%	0.00%	96.8%	2152.4 M	97.5%	1084.1 M	96.1%	1068.3 M	3.2%	71.5 M	89.0%	1980.3 M	8.3%	184.3 M	91.7%	88.5%	1968.1 M	95.8%	2131.1 M	94.4%	2099.9 M	1.40%	31.22 M	0.96%	21.28 M	1.26%	26.94 M	0.95%	20.29 M	2.9%	31.0 M	2.7%	28.4 M	145.4	349.9	347	163.3	323400.4 Mb	161614.5 Mb	161785.9 Mb	48.7%	157613.7 Mb	48.0%	155338.8 Mb	0.7%	1161.9 Mb	1.3%	0.6%	905.4 Mb	0.7%	0.5%	809.6 Mb	0.7%	90.2%	291571.2 Mb	91.9%	148476.9 Mb	88.5%	143094.3 Mb	82.9%	268009.2 Mb	2159.4 M	0.00%	7.00 M
SC501111	100.0%	2514.8 M	100.0%	2514.8 M	0.0%	0.00%	96.5%	2425.8 M	97.2%	1222.4 M	95.7%	1203.3 M	3.5%	89.0 M	88.4%	2223.9 M	11.9%	299.7 M	88.1%	84.5%	2126.1 M	95.4%	2398.2 M	93.9%	2360.5 M	1.50%	37.78 M	1.09%	27.52 M	1.36%	32.65 M	1.06%	25.31 M	3.1%	37.5 M	2.8%	34.1 M	145.8	381.5	385	165.6	366659.3 Mb	182966.7 Mb	183692.7 Mb	48.7%	178477.7 Mb	47.9%	175681.2 Mb	0.8%	1353.1 Mb	1.3%	0.6%	1052.3 Mb	0.8%	0.5%	926.1 Mb	0.7%	90.1%	330506.7 Mb	92.2%	168693.1 Mb	88.1%	161813.6 Mb	79.7%	292120.0 Mb	2433.9 M	0.00%	8.11 M
SD162355	100.0%	2694.6 M	100.0%	2694.6 M	0.0%	0.00%	96.3%	2595.7 M	97.0%	1306.9 M	95.7%	1288.8 M	3.7%	98.9 M	88.4%	2381.4 M	10.4%	280.9 M	89.6%	85.9%	2314.9 M	95.4%	2570.3 M	93.8%	2528.0 M	1.57%	42.22 M	0.95%	25.49 M	1.46%	37.44 M	1.21%	30.99 M	2.9%	38.4 M	2.7%	34.8 M	142.8	333.8	326	169.6	384892.7 Mb	192024.2 Mb	192868.5 Mb	48.5%	186710.1 Mb	47.9%	184306.0 Mb	0.8%	1551.3 Mb	1.4%	0.5%	919.5 Mb	0.6%	0.4%	796.2 Mb	0.5%	91.7%	352798.7 Mb	93.1%	178766.4 Mb	90.2%	174032.3 Mb	82.1%	316110.5 Mb	2606.5 M	0.00%	10.78 M
SD162357	100.0%	2583.1 M	100.0%	2583.1 M	0.0%	0.00%	96.6%	2495.0 M	97.2%	1255.5 M	96.0%	1239.5 M	3.4%	88.1 M	89.0%	2297.8 M	18.1%	467.7 M	81.9%	78.5%	2027.3 M	95.7%	2471.5 M	94.2%	2434.5 M	1.43%	37.04 M	0.91%	23.45 M	1.30%	32.25 M	1.08%	26.68 M	3.0%	37.8 M	2.8%	34.1 M	146.0	389.2	390	172.2	377045.0 Mb	188018.4 Mb	189026.6 Mb	48.7%	183624.2 Mb	48.1%	181295.0 Mb	0.7%	1357.9 Mb	1.1%	0.5%	857.1 Mb	0.6%	0.4%	739.0 Mb	0.5%	92.1%	347280.4 Mb	93.6%	175969.2 Mb	90.6%	171311.3 Mb	75.5%	284751.3 Mb	2503.2 M	0.00%	8.26 M
SD162359	100.0%	2751.1 M	100.0%	2751.1 M	0.0%	0.00%	96.8%	2661.7 M	97.3%	1338.7 M	96.2%	1323.0 M	3.2%	89.4 M	89.3%	2457.4 M	9.6%	265.2 M	90.4%	87.1%	2396.5 M	96.0%	2639.8 M	94.8%	2609.3 M	1.11%	30.52 M	0.80%	21.89 M	1.01%	26.76 M	0.83%	21.83 M	2.9%	38.4 M	2.6%	35.0 M	142.6	306.9	296	160.6	392305.7 Mb	195972.8 Mb	196332.9 Mb	48.6%	190781.2 Mb	48.1%	188631.5 Mb	0.8%	1441.0 Mb	1.1%	0.5%	885.8 Mb	0.5%	0.4%	764.4 Mb	0.4%	92.5%	363005.3 Mb	93.3%	182901.0 Mb	91.7%	180104.3 Mb	83.6%	327812.6 Mb	2670.8 M	0.00%	9.05 M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-mapping-metrics-table

Sort	Group	Column	Description	ID	Scale
\|\|	Mapping	Input reads	Total number of reads in this RG	`Total reads in RG pct`	None
\|\|	Mapping	M Input reads	Total number of reads in this RG, millions	`Total reads in RG`	read_count
\|\|	Mapping	Paired	% of reads with a mate sequenced	`Reads with mate sequenced pct`	None
\|\|	Mapping	M Paired	Number of reads with a mate sequenced, millions	`Reads with mate sequenced`	read_count
\|\|	Mapping	Single	% of reads without a mate sequenced	`Reads without mate sequenced pct`	None
\|\|	Mapping	M Single	Number of reads without a mate sequenced, millions	`Reads without mate sequenced`	read_count
\|\|	Mapping	QC-fail	% of reads not passing platform/vendor quality checks (SAM flag 0x200)	`QC-failed reads pct`	None
\|\|	Mapping	M QC-fail	Number of reads not passing platform/vendor quality checks (SAM flag 0x200), millions	`QC-failed reads`	read_count
\|\|	Mapping	Map	% of mapped reads	`Mapped reads pct`	None
\|\|	Mapping	M Map	Number of mapped reads, millions	`Mapped reads`	read_count
\|\|	Mapping	Map R1	% of mapped reads R1	`Mapped reads R1 pct`	None
\|\|	Mapping	M Map R1	Number of mapped reads R1, millions	`Mapped reads R1`	read_count
\|\|	Mapping	Map R2	% of mapped reads R2	`Mapped reads R2 pct`	None
\|\|	Mapping	M Map R2	Number of mapped reads R2, millions	`Mapped reads R2`	read_count
\|\|	Mapping	Unmap	% of unmapped reads	`Unmapped reads pct`	None
\|\|	Mapping	M Unmap	Number of unmapped reads, millions	`Unmapped reads`	read_count
\|\|	Mapping	MQ⩾40	% of reads with MAPQ [40:inf)	`Reads with MAPQ [40:inf) pct`	None
\|\|	Mapping	M MQ⩾40	Number of reads with MAPQ [40:inf), millions	`Reads with MAPQ [40:inf)`	read_count
\|\|	Mapping	Dup	% of duplicate marked reads as a result of the --enable-duplicatemarking option being used	`Number of duplicate marked reads pct`	None
\|\|	Mapping	M Dup	Number of duplicate marked reads as a result of the --enable-duplicatemarking option being used, millions	`Number of duplicate marked reads`	read_count
\|\|	Mapping	Uniq	% of unique reads (all reads minus duplicate marked reads)	`Number of unique reads (excl. duplicate marked reads) pct`	None
\|\|	Mapping	Uniq map	% of unique & mapped reads (mapped reads minus duplicate marked reads)	`Number of unique & mapped reads (excl. duplicate marked reads) pct`	None
\|\|	Mapping	M Uniq map	Number of unique & mapped reads (mapped reads minus duplicate marked reads), millions	`Number of unique & mapped reads (excl. duplicate marked reads)`	read_count
\|\|	Mapping	Self & mate map	% of reads mapped in pairs (itself & mate mapped)	`Paired reads (itself & mate mapped) pct`	None
\|\|	Mapping	M Self & mate map	Number of reads mapped in pairs (itself & mate mapped), millions	`Paired reads (itself & mate mapped)`	read_count
\|\|	Mapping	Prop pair	% of properly paired reads (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`Properly paired reads pct`	None
\|\|	Mapping	M Prop pair	Number of properly paired reads, millions (both reads in pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution). Duplicate and low quality reads are not excluded, i.e. the percentage is calculated relative to the total number of reads.	`Properly paired reads`	read_count
\|\|	Mapping	Discord	% of discordant reads: paired reads minus properly paired reads	`Not properly paired reads (discordant) pct`	None
\|\|	Mapping	M Discord	Number of discordant reads: paired reads minus properly paired reads , millions	`Not properly paired reads (discordant)`	read_count
\|\|	Mapping	Singleton	% of singleton reads: itself mapped; mate unmapped	`Singleton reads (itself mapped; mate unmapped) pct`	None
\|\|	Mapping	M Singleton	Number of singleton reads: itself mapped; mate unmapped, millions	`Singleton reads (itself mapped; mate unmapped)`	read_count
\|\|	Mapping	Diff chrom	% of paired reads with a mate mapped to a different chromosome	`Paired reads mapped to different chromosomes pct`	None
\|\|	Mapping	M Diff chrom	Number of paired reads with a mate mapped to a different chromosome, millions	`Paired reads mapped to different chromosomes`	read_count
\|\|	Mapping	Diff chr, MQ⩾10	% of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome	`Paired reads mapped to different chromosomes (MAPQ>=10) pct`	None
\|\|	Mapping	M Diff chr, MQ⩾10	Number of paired reads, mapped with MAPQ>=10 and with a mate mapped to a different chromosome, millions	`Paired reads mapped to different chromosomes (MAPQ>=10)`	read_count
\|\|	Mapping	Reads with indel R1	% of R1 reads containing at least 1 indel	`Reads with indel R1 pct`	None
\|\|	Mapping	M Reads with indel R1	Number of R1 reads containing at least 1 indel, millions	`Reads with indel R1`	read_count
\|\|	Mapping	Reads with indel R2	% of R2 reads containing at least 1 indel	`Reads with indel R2 pct`	None
\|\|	Mapping	M Reads with indel R2	Number of R2 reads containing at least 1 indel, millions	`Reads with indel R2`	read_count
\|\|	Mapping	Read len	Estimated read length. Total number of input bases divided by the number of reads	`Estimated read length`	None
\|\|	Mapping	Avg IS	Mean insert size	`Insert length: mean`	None
\|\|	Mapping	Med IS	Median insert size	`Insert length: median`	None
\|\|	Mapping	IS std	Standard deviation of insert size deviation	`Insert length: standard deviation`	None
\|\|	Mapping	Mb Input bases	Total number of bases sequenced, millions	`Total bases`	base_count
\|\|	Mapping	Mb Input bases R1	Total number of bases sequenced on R1 reads, millions	`Total bases R1`	base_count
\|\|	Mapping	Mb Input bases R2	Total number of bases sequenced on R2 reads, millions	`Total bases R2`	base_count
\|\|	Mapping	Mapped bases R1	% of mapped bases on R1 reads	`Mapped bases R1 pct`	None
\|\|	Mapping	Mb Mapped bases R1	Number of mapped bases on R1 reads, millions	`Mapped bases R1`	base_count
\|\|	Mapping	Mapped bases R2	% of mapped bases on R2 reads	`Mapped bases R2 pct`	None
\|\|	Mapping	Mb Mapped bases R2	Number of mapped bases on R2 reads, millions	`Mapped bases R2`	base_count
\|\|	Mapping	Soft-clip bases R1	% of soft-clipped bases on R1 reads	`Soft-clipped bases R1 pct`	None
\|\|	Mapping	Mb Soft-clip bases R1	Number of soft-clipped bases on R1 reads, millions	`Soft-clipped bases R1`	base_count
\|\|	Mapping	Soft-clip bases R2	% of soft-clipped bases on R2 reads	`Soft-clipped bases R2 pct`	None
\|\|	Mapping	MM bases R1	% of mismatched bases on R1, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1 pct`	None
\|\|	Mapping	Mb MM bases R1	Number of mismatched bases on R1, millions, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1`	base_count
\|\|	Mapping	MM bases R2	% of mismatched bases on R2, which is the sum of SNP count and indel lengths. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R2 pct`	None
\|\|	Mapping	MM bases R1 excl indels	% of mismatched bases on R1. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1 (excl. indels) pct`	None
\|\|	Mapping	Mb MM bases R1 excl indels	Number of mismatched bases on R1, millions. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R1 (excl. indels)`	base_count
\|\|	Mapping	MM bases R2 excl indels	% of mismatched bases on R2. The indels lengts are ignored. It does not count anything within soft clipping, or RNA introns. It also does not count a mismatch if either the reference base or read base is N	`Mismatched bases R2 (excl. indels) pct`	None
\|\|	Mapping	Q30	% of raw bases with BQ >= 30	`Q30 bases pct`	None
\|\|	Mapping	Mb Q30	Number of raw bases with BQ >= 30, millions	`Q30 bases`	base_count
\|\|	Mapping	Q30 R1	% of raw bases on R1 reads with BQ >= 30	`Q30 bases R1 pct`	None
\|\|	Mapping	Mb Q30 R1	Number of raw bases on R1 reads with BQ >= 30, millions	`Q30 bases R1`	base_count
\|\|	Mapping	Q30 R2	% of raw bases on R2 reads with BQ >= 30	`Q30 bases R2 pct`	None
\|\|	Mapping	Mb Q30 R2	Number of raw bases on R2 reads with BQ >= 30, millions	`Q30 bases R2`	base_count
\|\|	Mapping	Q30 excl dup & clipped	% of non-clipped bases with BQ >= 30 on non-duplicate reads	`Q30 bases (excl. dups & clipped bases) pct`	None
\|\|	Mapping	Mb Q30 excl dup & clipped	Number of non-clipped bases with BQ >= 30 on non-duplicate reads, millions	`Q30 bases (excl. dups & clipped bases)`	base_count
\|\|	Mapping	M Alignments	Total number of alignments with MQ > 0, millions	`Total alignments`	read_count
\|\|	Mapping	Sec'ry	% of secondary alignments. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`Secondary alignments pct`	None
\|\|	Mapping	M Sec'ry	Number of secondary alignments, millions. Secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".	`Secondary alignments`	read_count
\|\|	Mapping	M Suppl'ry	Number of supplementary (chimeric) alignments, millions. A chimeric read is split over multiple loci (possibly due to structural variants). One alignment is referred to as the representative alignment, the other are supplementary	`Supplementary (chimeric) alignments`	read_count

Mapped / paired / duplicated

Distribution of reads based on pairing, duplication and mapping.

Created with MultiQC

Variant calling

Variant calling metrics. Metrics are reported for each sample in multi sample VCF and gVCF files. Based on the run case, metrics are reported either as standard VARIANT CALLER or JOINT CALLER. All metrics are reported for post-filter VCFs, except for the "Filtered" metrics which represent how many variants were filtered out from pre-filter VCF to generate the post-filter VCF.

Showing ⁹/₉ rows and ⁹/₃₁ columns.

Sample Name	Variants	Variants	Biallelic	Biallelic	Multiallelic	Multiallelic	SNP	SNP	Indel	Indel	Ins	Ins	Del	Del	Hom ins	Hom ins	Het ins	Het ins	Hom del	Hom del	Het del	Het del	Het indel	Het indel	Ti/Tv	Het	Hom	Het/Hom	Callability	Autosome callability	M VC reads
SC501095	100.0%	4849223	98.1%	4757052	1.9%	92171	80.4%	3900154	18.5%	899140	9.3%	449413	9.3%	449727	3.3%	161012	6.0%	288401	3.4%	163022	5.9%	286705	0.5%	25002	2.0	2872860	1867305	1.5	NA	NA	2316.1 M
SC501096	100.0%	4904207	98.1%	4809561	1.9%	94646	80.4%	3944868	19.0%	933523	9.5%	466992	9.5%	466531	3.4%	166602	6.1%	300390	3.4%	168706	6.1%	297825	0.5%	25816	2.0	2982212	1921995	1.6	NA	NA	2170.4 M
SC501105	100.0%	4885301	98.1%	4790320	1.9%	94981	80.4%	3927275	19.1%	932239	9.5%	466027	9.5%	466212	3.4%	165319	6.2%	300708	3.4%	167590	6.1%	298622	0.5%	25787	2.0	2984076	1901225	1.6	NA	NA	2311.6 M
SC501108	100.0%	4867227	98.1%	4775190	1.9%	92037	80.5%	3915796	18.5%	901348	9.3%	450582	9.3%	450766	3.2%	157870	6.0%	292712	3.3%	160113	6.0%	290653	0.5%	25129	2.0	2917494	1839626	1.6	NA	NA	2181.9 M
SC501110	100.0%	4884094	98.1%	4790166	1.9%	93928	80.4%	3927186	19.1%	931315	9.5%	465363	9.5%	465952	3.4%	166358	6.1%	299005	3.5%	168367	6.1%	297585	0.5%	25593	2.0	2968632	1915462	1.6	NA	NA	1947.3 M
SC501111	100.0%	4844316	98.1%	4752255	1.9%	92061	80.4%	3895660	18.5%	898452	9.3%	449032	9.3%	449420	3.3%	159035	6.0%	289997	3.3%	160947	6.0%	288473	0.5%	24836	2.0	2891153	1842530	1.6	NA	NA	2096.2 M
SD162355	100.0%	4896047	98.1%	4801576	1.9%	94471	80.4%	3938031	18.5%	907124	9.3%	453416	9.3%	453708	3.2%	157740	6.0%	295676	3.2%	159246	6.0%	294462	0.5%	25467	2.0	2946131	1838147	1.6	NA	NA	2281.8 M
SD162357	100.0%	4877362	98.1%	4783570	1.9%	93792	80.4%	3920613	18.6%	906244	9.3%	452002	9.3%	454242	3.3%	159878	6.0%	292124	3.3%	161321	6.0%	292921	0.5%	25494	2.0	2912123	1856289	1.6	NA	NA	1993.3 M
SD162359	100.0%	4946727	98.0%	4849009	2.0%	97718	80.5%	3979858	19.0%	940174	9.5%	469359	9.5%	470815	3.3%	163646	6.2%	305713	3.4%	165584	6.2%	305231	0.5%	26695	2.0	3052829	1893898	1.6	NA	NA	2356.1 M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-vc-metrics-table

Sort	Group	Column	Description	ID	Scale
\|\|	Variant calling	Variants	Total number of variants (SNPs + MNPs + INDELS).	`Total pct`	None
\|\|	Variant calling	Variants	Total number of variants (SNPs + MNPs + INDELS).	`Total`	None
\|\|	Variant calling	Biallelic	% of sites in a genome that contains two observed alleles, counting the reference as one, and therefore allowing for one variant allele	`Biallelic pct`	None
\|\|	Variant calling	Biallelic	Number of sites in a genome that contains two observed alleles, counting the reference as one, and therefore allowing for one variant allele	`Biallelic`	None
\|\|	Variant calling	Multiallelic	% of sites in the VCF that contain three or more observed alleles. The reference is counted as one, therefore allowing for two or more variant alleles	`Multiallelic pct`	None
\|\|	Variant calling	Multiallelic	Number of sites in the VCF that contain three or more observed alleles. The reference is counted as one, therefore allowing for two or more variant alleles	`Multiallelic`	None
\|\|	Variant calling	SNP	% of SNPs in the variant set. A variant is counted as an SNP when the reference, allele 1, and allele2 are all length 1	`SNPs pct`	None
\|\|	Variant calling	SNP	Number of SNPs in the variant set. A variant is counted as an SNP when the reference, allele 1, and allele2 are all length 1	`SNPs`	None
\|\|	Variant calling	Indel	% of insetions and deletions in the variant set.	`Indels pct`	None
\|\|	Variant calling	Indel	Number of insetions and deletions in the variant set.	`Indels`	None
\|\|	Variant calling	Ins	% of insetions in the variant set.	`Insertions pct`	None
\|\|	Variant calling	Ins	Number of insetions in the variant set.	`Insertions`	None
\|\|	Variant calling	Del	% of deletions in the variant set.	`Deletions pct`	None
\|\|	Variant calling	Del	Number of deletions in the variant set.	`Deletions`	None
\|\|	Variant calling	Hom ins	% of variants that contains homozygous insertions	`Insertions (Hom) pct`	None
\|\|	Variant calling	Hom ins	Number of variants that contains homozygous insertions	`Insertions (Hom)`	None
\|\|	Variant calling	Het ins	% of variants where both alleles are insertions, but not homozygous	`Insertions (Het) pct`	None
\|\|	Variant calling	Het ins	Number of variants where both alleles are insertions, but not homozygous	`Insertions (Het)`	None
\|\|	Variant calling	Hom del	% of variants that contains homozygous deletions	`Deletions (Hom) pct`	None
\|\|	Variant calling	Hom del	Number of variants that contains homozygous deletions	`Deletions (Hom)`	None
\|\|	Variant calling	Het del	% of variants where both alleles are deletion, but not homozygous	`Deletions (Het) pct`	None
\|\|	Variant calling	Het del	Number of variants where both alleles are deletion, but not homozygous	`Deletions (Het)`	None
\|\|	Variant calling	Het indel	% of variants where genotypes are either [insertion+deletion], [insertion+snp] or [deletion+snp].	`Indels (Het) pct`	None
\|\|	Variant calling	Het indel	Number of variants where genotypes are either [insertion+deletion], [insertion+snp] or [deletion+snp].	`Indels (Het)`	None
\|\|	Variant calling	Ti/Tv	Ti/Tv ratio: ratio of transitions to transitions.	`Ti/Tv ratio`	None
\|\|	Variant calling	Het	Number of heterozygous variants	`Heterozygous`	None
\|\|	Variant calling	Hom	Number of homozygous variants	`Homozygous`	None
\|\|	Variant calling	Het/Hom	Heterozygous/ homozygous ratio	`Het/Hom ratio`	None
\|\|	Variant calling	Callability	Available only in germline mode with gVCF output. The percentage of non-N reference	`Percent Callability`	None
\|\|	Variant calling	Autosome callability	Available only in germline mode with gVCF output. The percentage of non-N reference	`Percent Autosome Callability`	None
\|\|	Variant calling	M VC reads	The number of reads used for variant calling, excluding any duplicate marked reads and reads falling outside of the target region	`Reads Processed`	read_count

Target Bed Coverage Metrics

Coverage metrics over target Bed. All samples are based on the target_bed.

Press the Help button for details.

The following criteria are used when calculating coverage:

Duplicate reads and clipped bases are ignored.
DRAGEN V3.4 - 3.7: Only reads with MAPQ > min MAPQ and bases with BQ > min BQ are considered
DRAGEN V3.8 - 4.1: By default, reads with MAPQ < 1 and bases with BQ < 0 are ignored. You can use the qc-coverage-filters-n option to specify which BQ bases and MAPQ reads to filter out.

Considering only bases usable for variant calling, i.e. excluding:

Clipped bases
Bases in duplicate reads
Reads with MAPQ < min MAPQ (default 20)
Bases with BQ < min BQ (default 10)
Reads with MAPQ = 0 (multimappers)
Overlapping mates are double-counted

Each _coverage_metrics.csv file may have an associated _overall_mean_cov.csv file. The latter contains the 'Average alignment coverage over <source file>' metric. Information about <source file>s can be found in the section's description or in this drop-list below if the produced text is long. If input directory does not contain _overall_mean_cov files, then "No 'coverage bed/target bed/wgs' source file found" is printed.

Showing ⁹/₉ rows and ⁵/₃₆ columns.

Sample Name	M Aln reads	M Reads on target	Reads on target	Mb Aln bases	Mb Bases on target	Bases on target	X cov	Y cov	Depth	Uniformity(>0.2×mean)	Uniformity(>0.4×mean)	Mean aut cov	Med aut cov	Mean/med autosomal coverage	≥1500x	≥1000x	≥500x	≥100x	≥50x	≥20x	≥15x	≥10x	≥3x	≥1x	≥0x	[500x:1000x)	[100x:500x)	[50x:100x)	[20x:50x)	[15x:20x)	[10x:15x)	[3x:10x)	[1x:3x)	0x
SC501095	2206.5	2195.9	99.5 %	314731.2	313231.3	99.5 %	55.79 x	47.73 x	107.13 x	97.15 %	96.27 %	110.54 x	114.00 x	0.97 x	0.01 %	0.01 %	0.02 %	75.13 %	95.29 %	97.22 %	97.41 %	97.63 %	98.17 %	98.60 %	100.00 %	0.01 %	75.11 %	20.16 %	1.93 %	0.18 %	0.23 %	0.53 %	0.43 %	1.40 %
SC501096	2083.9	2073.7	99.5 %	303304.7	301849.0	99.5 %	102.33 x	0.59 x	103.24 x	96.63 %	96.03 %	104.18 x	108.00 x	0.96 x	0.00 %	0.01 %	0.02 %	67.72 %	95.76 %	96.66 %	96.84 %	97.07 %	97.60 %	98.05 %	100.00 %	0.01 %	67.70 %	28.05 %	0.90 %	0.18 %	0.22 %	0.53 %	0.45 %	1.95 %
SC501105	2208.2	2197.2	99.5 %	312665.2	311124.5	99.5 %	105.46 x	0.99 x	106.41 x	96.61 %	96.04 %	107.38 x	111.00 x	0.97 x	0.01 %	0.01 %	0.02 %	73.68 %	95.83 %	96.68 %	96.86 %	97.08 %	97.60 %	98.02 %	100.00 %	0.01 %	73.66 %	22.15 %	0.85 %	0.18 %	0.22 %	0.52 %	0.43 %	1.98 %
SC501108	2082.2	2070.4	99.4 %	300705.4	299044.4	99.5 %	53.13 x	45.04 x	102.28 x	97.17 %	96.29 %	105.55 x	109.00 x	0.97 x	0.01 %	0.01 %	0.02 %	66.32 %	94.78 %	97.21 %	97.40 %	97.64 %	98.22 %	98.68 %	100.00 %	0.01 %	66.30 %	28.46 %	2.43 %	0.19 %	0.24 %	0.58 %	0.46 %	1.32 %
SC501110	1859.5	1851.6	99.6 %	268686.0	267552.7	99.6 %	91.23 x	0.60 x	91.51 x	96.62 %	96.05 %	92.31 x	95.00 x	0.97 x	0.00 %	0.01 %	0.02 %	33.41 %	95.53 %	96.59 %	96.78 %	97.01 %	97.55 %	97.99 %	100.00 %	0.01 %	33.40 %	62.12 %	1.06 %	0.19 %	0.24 %	0.54 %	0.44 %	2.01 %
SC501111	2001.8	1990.7	99.5 %	290192.3	288618.5	99.5 %	51.14 x	41.95 x	98.72 x	97.20 %	96.27 %	101.89 x	105.00 x	0.97 x	0.01 %	0.01 %	0.02 %	58.73 %	94.31 %	97.20 %	97.39 %	97.62 %	98.17 %	98.61 %	100.00 %	0.01 %	58.71 %	35.59 %	2.88 %	0.19 %	0.23 %	0.55 %	0.44 %	1.39 %
SD162355	2178.1	2162.5	99.3 %	308900.6	306712.0	99.3 %	52.64 x	42.96 x	104.90 x	97.10 %	96.04 %	108.39 x	112.00 x	0.97 x	0.01 %	0.01 %	0.02 %	70.02 %	94.54 %	97.13 %	97.31 %	97.54 %	98.08 %	98.52 %	100.00 %	0.01 %	70.00 %	24.51 %	2.60 %	0.18 %	0.23 %	0.54 %	0.44 %	1.48 %
SD162357	1905.5	1889.2	99.1 %	276178.1	273838.6	99.2 %	46.84 x	38.56 x	93.66 x	97.18 %	95.98 %	96.78 x	100.00 x	0.97 x	0.01 %	0.01 %	0.02 %	44.00 %	93.05 %	97.14 %	97.34 %	97.57 %	98.12 %	98.57 %	100.00 %	0.01 %	43.98 %	49.05 %	4.09 %	0.20 %	0.24 %	0.55 %	0.44 %	1.43 %
SD162359	2265.5	2245.1	99.1 %	320819.8	317963.4	99.1 %	102.45 x	0.90 x	108.75 x	96.54 %	95.95 %	110.04 x	113.00 x	0.97 x	0.00 %	0.01 %	0.02 %	77.32 %	95.77 %	96.61 %	96.78 %	97.00 %	97.52 %	97.95 %	100.00 %	0.01 %	77.30 %	18.45 %	0.84 %	0.17 %	0.22 %	0.52 %	0.44 %	2.05 %

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-cov-metrics-own-section-target-bed-table

Sort	Group	Column	Description	ID	Scale
\|\|	Coverage	M Aln reads	Total number (millions) of aligned reads.	`target bed aligned reads`	None
\|\|	Coverage	M Reads on target	Number (millions) of uniquely mapped reads to target region. DRAGEN V3.4 - V3.8: When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region. DRAGEN V3.9 - V4.1: Only reads with MAPQ >= 1 are included. Secondary and supplementary alignments are ignored.	`target bed aligned reads in target region`	None
\|\|	Coverage	Reads on target	Number of uniquely mapped reads to target region relative to the number of uniquely mapped reads to the genome.	`target bed aligned reads in target region pct`	None
\|\|	Coverage	Mb Aln bases	Total number (millions) of aligned bases.	`target bed aligned bases`	None
\|\|	Coverage	Mb Bases on target	Number (millions) of uniquely mapped bases to target region.	`target bed aligned bases in target region`	None
\|\|	Coverage	Bases on target	Number (millions) of uniquely mapped bases to target region relative to the number of uniquely mapped bases to the genome.	`target bed aligned bases in target region pct`	None
\|\|	Coverage	X cov	Total number of bases that aligned to the intersection of chromosome X with target region divided by the total number of loci in the intersection of chromosome X with target region. If there is no chromosome X in the reference genome or the target region does not intersect chromosome X this metric shows as NA.	`target bed average chr x coverage over target region`	None
\|\|	Coverage	Y cov	Total number of bases that aligned to the intersection of chromosome Y with target region divided by the total number of loci in the intersection of chromosome Y with target region. If there is no chromosome Y in the reference genome or the target region does not intersect chromosome Y this metric shows as NA.	`target bed average chr y coverage over target region`	None
\|\|	Coverage	Depth	Coverage depth over target region: number of uniquely mapped bases to target region divided by the number of sites in target region.	`target bed average alignment coverage over target region`	None
\|\|	Coverage	MT cov	Total number of bases that aligned to the intersection of the mitochondrial chromosome with target region divided by the total number of loci in the intersection of the mitochondrial chromosome with target region. If there is no mitochondrial chromosome in the reference genome or the target region does not intersect mitochondrial chromosome, this metric shows as NA.	`target bed average mitochondrial coverage over target region`	None
\|\|	Coverage	Uniformity(>0.2×mean)	Percentage of sites with coverage greater than 20.0% of the mean coverage in target region. Demonstrates the uniformity of coverage, the higher the better.	`target bed uniformity of coverage (pct > 0 2*mean) over target region`	None
\|\|	Coverage	Uniformity(>0.4×mean)	Percentage of sites with coverage greater than 40.0% of the mean coverage in target region.	`target bed uniformity of coverage (pct > 0 4*mean) over target region`	None
\|\|	Coverage	Mean aut cov	Total number of bases that aligned to the autosomal loci in target region divided by the total number of loci in the autosomal loci in target region. If there is no autosome in the reference genome, or the target region does not intersect autosomes, this metric shows as NA.	`target bed average autosomal coverage over target region`	None
\|\|	Coverage	Med aut cov	Median alignment coverage over the autosomal loci in target region. If there is no autosome in the reference genome or the target region does not intersect autosomes, this metric shows as NA.	`target bed median autosomal coverage over target region`	None
\|\|	Coverage	Mean/med autosomal coverage	Mean autosomal coverage in target region divided by the median autosomal coverage in target region. If there is no autosome in the reference genome or the target region does not intersect autosomes, this metric shows as NA.	`target bed mean/median autosomal coverage ratio over target region`	None
\|\|	Coverage	≥1500x	Percentage of sites in target region with at least 1500x coverage.	`target bed pct of target region with coverage [1500x:inf)`	None
\|\|	Coverage	≥1000x	Percentage of sites in target region with at least 1000x coverage.	`target bed pct of target region with coverage [1000x:inf)`	None
\|\|	Coverage	≥500x	Percentage of sites in target region with at least 500x coverage.	`target bed pct of target region with coverage [500x:inf)`	None
\|\|	Coverage	≥100x	Percentage of sites in target region with at least 100x coverage.	`target bed pct of target region with coverage [100x:inf)`	None
\|\|	Coverage	≥50x	Percentage of sites in target region with at least 50x coverage.	`target bed pct of target region with coverage [50x:inf)`	None
\|\|	Coverage	≥20x	Percentage of sites in target region with at least 20x coverage.	`target bed pct of target region with coverage [20x:inf)`	None
\|\|	Coverage	≥15x	Percentage of sites in target region with at least 15x coverage.	`target bed pct of target region with coverage [15x:inf)`	None
\|\|	Coverage	≥10x	Percentage of sites in target region with at least 10x coverage.	`target bed pct of target region with coverage [10x:inf)`	None
\|\|	Coverage	≥3x	Percentage of sites in target region with at least 3x coverage.	`target bed pct of target region with coverage [3x:inf)`	None
\|\|	Coverage	≥1x	Percentage of sites in target region with at least 1x coverage.	`target bed pct of target region with coverage [1x:inf)`	None
\|\|	Coverage	≥0x	Percentage of sites in target region with any coverage.	`target bed pct of target region with coverage [0x:inf)`	None
\|\|	Coverage	[1000x:1500x)	Percentage of sites in target region with at least 1000x but less than 1500x coverage.	`target bed pct of target region with coverage [1000x:1500x)`	None
\|\|	Coverage	[500x:1000x)	Percentage of sites in target region with at least 500x but less than 1000x coverage.	`target bed pct of target region with coverage [500x:1000x)`	None
\|\|	Coverage	[100x:500x)	Percentage of sites in target region with at least 100x but less than 500x coverage.	`target bed pct of target region with coverage [100x:500x)`	None
\|\|	Coverage	[50x:100x)	Percentage of sites in target region with at least 50x but less than 100x coverage.	`target bed pct of target region with coverage [50x:100x)`	None
\|\|	Coverage	[20x:50x)	Percentage of sites in target region with at least 20x but less than 50x coverage.	`target bed pct of target region with coverage [20x:50x)`	None
\|\|	Coverage	[15x:20x)	Percentage of sites in target region with at least 15x but less than 20x coverage.	`target bed pct of target region with coverage [15x:20x)`	None
\|\|	Coverage	[10x:15x)	Percentage of sites in target region with at least 10x but less than 15x coverage.	`target bed pct of target region with coverage [10x:15x)`	None
\|\|	Coverage	[3x:10x)	Percentage of sites in target region with at least 3x but less than 10x coverage.	`target bed pct of target region with coverage [3x:10x)`	None
\|\|	Coverage	[1x:3x)	Percentage of sites in target region with at least 1x but less than 3x coverage.	`target bed pct of target region with coverage [1x:3x)`	None
\|\|	Coverage	0x	Percentage of sites in target region with no coverage.	`target bed pct of target region with coverage [0x:1x)`	None

WGS Coverage Metrics

Coverage metrics over genome. All samples are based on the wgs.

Press the Help button for details.

The following criteria are used when calculating coverage:

Duplicate reads and clipped bases are ignored.
DRAGEN V3.4 - 3.7: Only reads with MAPQ > min MAPQ and bases with BQ > min BQ are considered
DRAGEN V3.8 - 4.1: By default, reads with MAPQ < 1 and bases with BQ < 0 are ignored. You can use the qc-coverage-filters-n option to specify which BQ bases and MAPQ reads to filter out.

Considering only bases usable for variant calling, i.e. excluding:

Clipped bases
Bases in duplicate reads
Reads with MAPQ < min MAPQ (default 20)
Bases with BQ < min BQ (default 10)
Reads with MAPQ = 0 (multimappers)
Overlapping mates are double-counted

Showing ⁹/₉ rows and ⁵/₃₆ columns.

Sample Name	M Aln reads	M Reads on target	Reads on target	Mb Aln bases	Mb Bases on target	Bases on target	X cov	Y cov	Depth	MT cov	Uniformity(>0.2×mean)	Uniformity(>0.4×mean)	Mean aut cov	Med aut cov	Mean/med autosomal coverage	≥1500x	≥1000x	≥500x	≥100x	≥50x	≥20x	≥15x	≥10x	≥3x	≥1x	≥0x	[1000x:1500x)	[500x:1000x)	[100x:500x)	[50x:100x)	[20x:50x)	[15x:20x)	[10x:15x)	[3x:10x)	[1x:3x)	0x
SC501095	2206.5	2206.5	100.0 %	314731.2	314731.2	100.0 %	55.79 x	47.73 x	104.10 x	10539.65 x	94.23 %	93.40 %	110.54 x	115.00 x	0.96 x	0.01 %	0.01 %	0.02 %	72.78 %	92.35 %	94.27 %	94.46 %	94.69 %	95.25 %	95.70 %	100.00 %	0.00 %	0.01 %	72.75 %	19.57 %	1.92 %	0.19 %	0.24 %	0.55 %	0.46 %	4.30 %
SC501096	2083.9	2083.9	100.0 %	303304.7	303304.7	100.0 %	102.33 x	0.59 x	100.34 x	13363.96 x	93.70 %	93.12 %	104.18 x	108.00 x	0.96 x	0.01 %	0.01 %	0.02 %	65.59 %	92.81 %	93.74 %	93.92 %	94.15 %	94.71 %	95.18 %	100.00 %	0.00 %	0.01 %	65.57 %	27.22 %	0.93 %	0.19 %	0.23 %	0.55 %	0.47 %	4.82 %
SC501105	2208.2	2208.2	100.0 %	312665.2	312665.2	100.0 %	105.46 x	0.99 x	103.41 x	15866.96 x	93.69 %	93.09 %	107.38 x	111.00 x	0.97 x	0.01 %	0.01 %	0.02 %	71.35 %	92.84 %	93.72 %	93.91 %	94.14 %	94.67 %	95.12 %	100.00 %	0.00 %	0.01 %	71.33 %	21.49 %	0.88 %	0.19 %	0.23 %	0.54 %	0.45 %	4.88 %
SC501108	2082.2	2082.2	100.0 %	300705.4	300705.4	100.0 %	53.13 x	45.04 x	99.47 x	10950.75 x	94.27 %	93.43 %	105.55 x	109.00 x	0.97 x	0.01 %	0.01 %	0.02 %	64.25 %	91.86 %	94.27 %	94.46 %	94.71 %	95.31 %	95.80 %	100.00 %	0.00 %	0.01 %	64.22 %	27.61 %	2.41 %	0.20 %	0.25 %	0.60 %	0.48 %	4.20 %
SC501110	1859.5	1859.5	100.0 %	268686.0	268686.0	100.0 %	91.23 x	0.60 x	88.91 x	10184.05 x	93.77 %	93.17 %	92.31 x	96.00 x	0.96 x	0.01 %	0.01 %	0.02 %	32.39 %	92.60 %	93.69 %	93.89 %	94.13 %	94.69 %	95.15 %	100.00 %	0.00 %	0.01 %	32.38 %	60.21 %	1.09 %	0.20 %	0.24 %	0.56 %	0.46 %	4.85 %
SC501111	2001.8	2001.8	100.0 %	290192.3	290192.3	100.0 %	51.14 x	41.95 x	95.98 x	10979.28 x	94.25 %	93.41 %	101.89 x	106.00 x	0.96 x	0.01 %	0.01 %	0.02 %	56.89 %	91.39 %	94.25 %	94.44 %	94.68 %	95.25 %	95.71 %	100.00 %	0.00 %	0.01 %	56.87 %	34.51 %	2.86 %	0.19 %	0.24 %	0.57 %	0.46 %	4.29 %
SD162355	2178.1	2178.1	100.0 %	308900.6	308900.6	100.0 %	52.64 x	42.96 x	102.13 x	42381.73 x	94.10 %	93.15 %	108.39 x	112.00 x	0.97 x	0.01 %	0.02 %	0.03 %	67.78 %	91.56 %	94.14 %	94.33 %	94.56 %	95.12 %	95.58 %	100.00 %	0.01 %	0.01 %	67.75 %	23.78 %	2.58 %	0.19 %	0.23 %	0.56 %	0.46 %	4.42 %
SD162357	1905.5	1905.5	100.0 %	276178.1	276178.1	100.0 %	46.84 x	38.56 x	91.37 x	35360.02 x	94.24 %	93.20 %	96.78 x	100.00 x	0.97 x	0.01 %	0.01 %	0.02 %	42.64 %	90.19 %	94.20 %	94.41 %	94.65 %	95.22 %	95.69 %	100.00 %	0.00 %	0.01 %	42.61 %	47.55 %	4.02 %	0.20 %	0.25 %	0.57 %	0.46 %	4.31 %
SD162359	2265.5	2265.5	100.0 %	320819.8	320819.8	100.0 %	102.45 x	0.90 x	106.05 x	33320.05 x	93.55 %	92.96 %	110.04 x	114.00 x	0.97 x	0.01 %	0.01 %	0.02 %	74.83 %	92.74 %	93.62 %	93.80 %	94.02 %	94.56 %	95.01 %	100.00 %	0.00 %	0.01 %	74.80 %	17.92 %	0.87 %	0.18 %	0.23 %	0.53 %	0.46 %	4.99 %

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-cov-metrics-own-section-wgs-table

Sort	Group	Column	Description	ID	Scale
\|\|	Coverage	M Aln reads	Total number (millions) of aligned reads.	`wgs aligned reads`	None
\|\|	Coverage	M Reads on target	Number (millions) of uniquely mapped reads to genome. DRAGEN V3.4 - V3.8: When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region. DRAGEN V3.9 - V4.1: Only reads with MAPQ >= 1 are included. Secondary and supplementary alignments are ignored.	`wgs aligned reads in genome`	None
\|\|	Coverage	Reads on target	Number of uniquely mapped reads to genome relative to the number of uniquely mapped reads to the genome.	`wgs aligned reads in genome pct`	None
\|\|	Coverage	Mb Aln bases	Total number (millions) of aligned bases.	`wgs aligned bases`	None
\|\|	Coverage	Mb Bases on target	Number (millions) of uniquely mapped bases to genome.	`wgs aligned bases in genome`	None
\|\|	Coverage	Bases on target	Number (millions) of uniquely mapped bases to genome relative to the number of uniquely mapped bases to the genome.	`wgs aligned bases in genome pct`	None
\|\|	Coverage	X cov	Total number of bases that aligned to the intersection of chromosome X with genome divided by the total number of loci in the intersection of chromosome X with genome. If there is no chromosome X in the reference genome or the genome does not intersect chromosome X this metric shows as NA.	`wgs average chr x coverage over genome`	None
\|\|	Coverage	Y cov	Total number of bases that aligned to the intersection of chromosome Y with genome divided by the total number of loci in the intersection of chromosome Y with genome. If there is no chromosome Y in the reference genome or the genome does not intersect chromosome Y this metric shows as NA.	`wgs average chr y coverage over genome`	None
\|\|	Coverage	Depth	Coverage depth over genome: number of uniquely mapped bases to genome divided by the number of sites in genome.	`wgs average alignment coverage over genome`	None
\|\|	Coverage	MT cov	Total number of bases that aligned to the intersection of the mitochondrial chromosome with genome divided by the total number of loci in the intersection of the mitochondrial chromosome with genome. If there is no mitochondrial chromosome in the reference genome or the genome does not intersect mitochondrial chromosome, this metric shows as NA.	`wgs average mitochondrial coverage over genome`	None
\|\|	Coverage	Uniformity(>0.2×mean)	Percentage of sites with coverage greater than 20% of the mean coverage in genome. Demonstrates the uniformity of coverage, the higher the better.	`wgs uniformity of coverage (pct > 0 2*mean) over genome`	None
\|\|	Coverage	Uniformity(>0.4×mean)	Percentage of sites with coverage greater than 40.0% of the mean coverage in genome.	`wgs uniformity of coverage (pct > 0 4*mean) over genome`	None
\|\|	Coverage	Mean aut cov	Average autosomal coverage over genome. Calculated as the number of bases that aligned to the autosomal loci in genome divided by the total number of loci in the autosomal loci in genome. If there are no autosomes in the reference genome, or the region does not intersect autosomes, this metric shows as NA.	`wgs average autosomal coverage over genome`	None
\|\|	Coverage	Med aut cov	Median alignment coverage over the autosomal loci in genome. If there is no autosome in the reference genome or the genome does not intersect autosomes, this metric shows as NA.	`wgs median autosomal coverage over genome`	None
\|\|	Coverage	Mean/med autosomal coverage	Mean autosomal coverage in genome divided by the median autosomal coverage in genome. If there is no autosome in the reference genome or the genome does not intersect autosomes, this metric shows as NA.	`wgs mean/median autosomal coverage ratio over genome`	None
\|\|	Coverage	≥1500x	Percentage of sites in genome with at least 1500x coverage.	`wgs pct of genome with coverage [1500x:inf)`	None
\|\|	Coverage	≥1000x	Percentage of sites in genome with at least 1000x coverage.	`wgs pct of genome with coverage [1000x:inf)`	None
\|\|	Coverage	≥500x	Percentage of sites in genome with at least 500x coverage.	`wgs pct of genome with coverage [500x:inf)`	None
\|\|	Coverage	≥100x	Percentage of sites in genome with at least 100x coverage.	`wgs pct of genome with coverage [100x:inf)`	None
\|\|	Coverage	≥50x	Percentage of sites in genome with at least 50x coverage.	`wgs pct of genome with coverage [50x:inf)`	None
\|\|	Coverage	≥20x	Percentage of sites in genome with at least 20x coverage.	`wgs pct of genome with coverage [20x:inf)`	None
\|\|	Coverage	≥15x	Percentage of sites in genome with at least 15x coverage.	`wgs pct of genome with coverage [15x:inf)`	None
\|\|	Coverage	≥10x	Percentage of sites in genome with at least 10x coverage.	`wgs pct of genome with coverage [10x:inf)`	None
\|\|	Coverage	≥3x	Percentage of sites in genome with at least 3x coverage.	`wgs pct of genome with coverage [3x:inf)`	None
\|\|	Coverage	≥1x	Percentage of sites in genome with at least 1x coverage.	`wgs pct of genome with coverage [1x:inf)`	None
\|\|	Coverage	≥0x	Percentage of sites in genome with any coverage.	`wgs pct of genome with coverage [0x:inf)`	None
\|\|	Coverage	[1000x:1500x)	Percentage of sites in genome with at least 1000x but less than 1500x coverage.	`wgs pct of genome with coverage [1000x:1500x)`	None
\|\|	Coverage	[500x:1000x)	Percentage of sites in genome with at least 500x but less than 1000x coverage.	`wgs pct of genome with coverage [500x:1000x)`	None
\|\|	Coverage	[100x:500x)	Percentage of sites in genome with at least 100x but less than 500x coverage.	`wgs pct of genome with coverage [100x:500x)`	None
\|\|	Coverage	[50x:100x)	Percentage of sites in genome with at least 50x but less than 100x coverage.	`wgs pct of genome with coverage [50x:100x)`	None
\|\|	Coverage	[20x:50x)	Percentage of sites in genome with at least 20x but less than 50x coverage.	`wgs pct of genome with coverage [20x:50x)`	None
\|\|	Coverage	[15x:20x)	Percentage of sites in genome with at least 15x but less than 20x coverage.	`wgs pct of genome with coverage [15x:20x)`	None
\|\|	Coverage	[10x:15x)	Percentage of sites in genome with at least 10x but less than 15x coverage.	`wgs pct of genome with coverage [10x:15x)`	None
\|\|	Coverage	[3x:10x)	Percentage of sites in genome with at least 3x but less than 10x coverage.	`wgs pct of genome with coverage [3x:10x)`	None
\|\|	Coverage	[1x:3x)	Percentage of sites in genome with at least 1x but less than 3x coverage.	`wgs pct of genome with coverage [1x:3x)`	None
\|\|	Coverage	0x	Percentage of sites in genome with no coverage.	`wgs pct of genome with coverage [0x:1x)`	None

Coverage distribution

Number of locations in the reference genome with a given depth of coverage.

Bases of a reference sequence (y-axis) are groupped by their depth of coverage (0×, 1×, …, N×) (x-axis). This plot shows the frequency of coverage depths relative to the reference sequence for each read dataset, which provides an indirect measure of the level and variation of coverage depth in the corresponding sequenced sample.

If reads are randomly distributed across the reference sequence, this plot should resemble a Poisson distribution (Lander & Waterman 1988), with a peak indicating approximate depth of coverage, and more uniform coverage depth being reflected in a narrower spread. The optimal level of coverage depth depends on the aims of the experiment, though it should at minimum be sufficiently high to adequately address the biological question; greater uniformity of coverage is generally desirable, because it increases breadth of coverage for a given depth of coverage, allowing equivalent results to be achieved at a lower sequencing depth (Sampson et al. 2011; Sims et al. 2014). However, it is difficult to achieve uniform coverage depth in practice, due to biases introduced during sample preparation (van Dijk et al. 2014), sequencing (Ross et al. 2013) and read mapping (Sims et al. 2014).

This plot may include a small peak for regions of the reference sequence with zero depth of coverage. Such regions may be absent from the given sample (due to a deletion or structural rearrangement), present in the sample but not successfully sequenced (due to bias in sequencing or preparation), or sequenced but not successfully mapped to the reference (due to the choice of mapping algorithm, the presence of repeat sequences, or mismatches caused by variants or sequencing errors). Related factors cause most datasets to contain some unmapped reads (Sims et al. 2014).

Created with MultiQC

Cumulative coverage hist

Number of locations in the reference genome with at least given depth of coverage.

For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position, while the breadth of coverage is the fraction of the reference sequence to which reads have been mapped with at least a given depth of coverage (Sims et al. 2014).

Defining coverage breadth in terms of coverage depth is useful, because sequencing experiments typically require a specific minimum depth of coverage over the region of interest (Sims et al. 2014), so the extent of the reference sequence that is amenable to analysis is constrained to lie within regions that have sufficient depth. With inadequate sequencing breadth, it can be difficult to distinguish the absence of a biological feature (such as a gene) from a lack of data (Green 2007).

For increasing coverage depths (1×, 2×, …, N×), coverage breadth is calculated as the percentage of the reference sequence that is covered by at least that number of reads, then plots coverage breadth (y-axis) against coverage depth (x-axis). This plot shows the relationship between sequencing depth and breadth for each read dataset, which can be used to gauge, for example, the likely effect of a minimum depth filter on the fraction of a genome available for analysis.

Created with MultiQC

Coverage per contig

Average coverage per contig or chromosome. Calculated as the number of bases (excluding duplicate marked reads, reads with MAPQ=0, and clipped bases), divided by the length of the contig or (if a target bed is used) the total length of the target region spanning that contig.

Created with MultiQC

Coverage per contig (non-main)

Non-main contigs: unlocalized (random), unplaced (chrU), alts (*_alt), mitochondria (chrM), EBV, HLA. Zoom in to see more contigs as all labels don't fit the screen.

Created with MultiQC

Fragment length hist

Distribution of estimated fragment lengths of mapped reads per read group. Only points supported by at least 5 reads are shown to prevent long flat tail. The plot is also smoothed down to showing 300 points on the X axis to reduce noise.

Created with MultiQC

Trimmer Metrics

Metrics on trimmed reads.

Showing ⁹/₉ rows and ²²/₂₂ columns.

Sample Name	Total input reads	Total input bases	Total input bases R1	Total input bases R2	Average input read length	Remaining poly-G K-mers R2 3prime	Poly-G soft trimmed reads unfiltered R1 3prime	Poly-G soft trimmed reads unfiltered R2 3prime	Poly-G soft trimmed bases unfiltered R1 3prime	Poly-G soft trimmed bases unfiltered R2 3prime
SC501095	2554951260.0	365659479246.0	182671015190.0	182988464056.0	143.0	1.0	0.1	1.5	0.1	1.4
SC501096	2380036766.0	348283330343.0	174049534906.0	174233795437.0	146.0	1.1	0.1	1.6	0.0	1.5
SC501105	2617623186.0	372355127256.0	185951497273.0	186403629983.0	142.0	1.0	0.1	1.5	0.0	1.4
SC501108	2465729128.0	358404014957.0	179019948420.0	179384066537.0	145.0	1.1	0.1	1.6	0.0	1.5
SC501110	2223890036.0	323400398399.0	161614492216.0	161785906183.0	145.0	0.9	0.1	1.4	0.0	1.3
SC501111	2514803832.0	366659342143.0	182966652446.0	183692689697.0	145.0	1.4	0.1	1.9	0.0	1.8
SD162355	2694630052.0	384892728308.0	192024215197.0	192868513111.0	142.0	1.1	0.1	1.9	0.1	1.7
SD162357	2583116404.0	377045043113.0	188018447976.0	189026595137.0	145.0	1.4	0.1	1.9	0.1	1.8
SD162359	2751117024.0	392305678023.0	195972751622.0	196332926401.0	142.0	0.8	0.1	1.4	0.1	1.3

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: dragen-trimmer-metrics-table

Sort	Group	Column	Description	ID	Scale
\|\|	Trimmer Metrics	Total input reads	Total input reads	`Total input reads`	None
\|\|	Trimmer Metrics	Total input bases	Total input bases	`Total input bases`	None
\|\|	Trimmer Metrics	Total input bases R1	Total input bases R1	`Total input bases R1`	None
\|\|	Trimmer Metrics	Total input bases R2	Total input bases R2	`Total input bases R2`	None
\|\|	Trimmer Metrics	Average input read length	Average input read length	`Average input read length`	None
\|\|	Trimmer Metrics	Total trimmed reads	Total trimmed reads	`Total trimmed reads`	None
\|\|	Trimmer Metrics	Total trimmed bases	Total trimmed bases	`Total trimmed bases`	None
\|\|	Trimmer Metrics	Average bases trimmed per read	Average bases trimmed per read	`Average bases trimmed per read`	None
\|\|	Trimmer Metrics	Average bases trimmed per trimmed read	Average bases trimmed per trimmed read	`Average bases trimmed per trimmed read`	None
\|\|	Trimmer Metrics	Remaining poly-G K-mers R1 3prime	Remaining poly-G K-mers R1 3prime	`Remaining poly-G K-mers R1 3prime`	None
\|\|	Trimmer Metrics	Remaining poly-G K-mers R2 3prime	Remaining poly-G K-mers R2 3prime	`Remaining poly-G K-mers R2 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed reads unfiltered R1 3prime	Poly-G soft trimmed reads unfiltered R1 3prime	`Poly-G soft trimmed reads unfiltered R1 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed reads unfiltered R2 3prime	Poly-G soft trimmed reads unfiltered R2 3prime	`Poly-G soft trimmed reads unfiltered R2 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed reads filtered R1 3prime	Poly-G soft trimmed reads filtered R1 3prime	`Poly-G soft trimmed reads filtered R1 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed reads filtered R2 3prime	Poly-G soft trimmed reads filtered R2 3prime	`Poly-G soft trimmed reads filtered R2 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed bases unfiltered R1 3prime	Poly-G soft trimmed bases unfiltered R1 3prime	`Poly-G soft trimmed bases unfiltered R1 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed bases unfiltered R2 3prime	Poly-G soft trimmed bases unfiltered R2 3prime	`Poly-G soft trimmed bases unfiltered R2 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed bases filtered R1 3prime	Poly-G soft trimmed bases filtered R1 3prime	`Poly-G soft trimmed bases filtered R1 3prime`	None
\|\|	Trimmer Metrics	Poly-G soft trimmed bases filtered R2 3prime	Poly-G soft trimmed bases filtered R2 3prime	`Poly-G soft trimmed bases filtered R2 3prime`	None
\|\|	Trimmer Metrics	Total filtered reads	Total filtered reads	`Total filtered reads`	None
\|\|	Trimmer Metrics	Reads filtered for minimum read length R1	Reads filtered for minimum read length R1	`Reads filtered for minimum read length R1`	None
\|\|	Trimmer Metrics	Reads filtered for minimum read length R2	Reads filtered for minimum read length R2	`Reads filtered for minimum read length R2`	None

Time Metrics

Time metrics for DRAGEN run. Total run time is less than the sum of individual steps because of parallelization.

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DRAGEN-FastQC

DRAGEN-FastQC is a Bio-IT Platform that provides ultra-rapid secondary analysis of sequencing data using field-programmable gate array technology (FPGA).

Per-Position Mean Quality Scores

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

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Per-Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help: The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

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Sequence Length Distribution

The distribution of fragment sizes (read lengths) found. See the FastQC help

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Per-Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help: This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content. In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution. An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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GC Content Mean Quality Scores

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

Created with MultiQC

Per-Position N Content

The percentage of base calls at each position for which an N was called.

From the FastQC help: If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called. It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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Per-Position Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor. To see the data as a line plot, as in the original FastQC graph, click on a sample track. From the FastQC help: Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called. In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other. It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

Alignment Summary

Please note that Picard's read counts are divided by two for paired-end data. Total bases (including unaligned) is not provided.

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Mean read length

The mean read length of the set of reads examined.

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Base Distribution

Plot shows the distribution of bases by cycle.

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GC Coverage Bias

This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.

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Insert Size

Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

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Mark Duplicates

Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
READS_UNMAPPED = UNMAPPED_READS

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Mean Base Quality by Cycle

Plot shows the mean base quality by cycle.

This metric gives an overall snapshot of sequencing machine performance. For most types of sequencing data, the output is expected to show a slight reduction in overall base quality scores towards the end of each read.

Spikes in quality within reads are not expected and may indicate that technical problems occurred during sequencing.

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Base Quality Distribution

Plot shows the count of each base quality score.

Created with MultiQC

WGS Coverage

The number of bases in the genome territory for each fold coverage. Note that final 1% of data is hidden to prevent very long tails.

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WGS Filtered Bases

For more information about the filtered categories, see the Picard documentation.

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FastQ Screen

Version: 0.15.3

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.DOI: 10.12688/f1000research.15931.2.

Mapped Reads

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FastQC

Version: 0.12.1

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

Sequence Counts

Sequence counts for each sample. Duplicate read counts are an estimate only.

This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

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Sequence Quality Histograms

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

Created with MultiQC

Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

Created with MultiQC

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To see the data as a line plot, as in the original FastQC graph, click on a sample track.

From the FastQC help:

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

Created with MultiQC

Per Base N Content

The percentage of base calls at each position for which an N was called.

From the FastQC help:

If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

Created with MultiQC

Sequence Length Distribution

The distribution of fragment sizes (read lengths) found. See the FastQC help

Created with MultiQC

Sequence Duplication Levels

The relative level of duplication found for every sequence.

From the FastQC Help:

In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

Created with MultiQC

Overrepresented sequences by sample

The total amount of overrepresented sequences found in each library.

FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

From the FastQC Help:

A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

18 samples had less than 1% of reads made up of overrepresented sequences

Top overrepresented sequences

Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

Showing ⁰/₀ rows.

Overrepresented sequence

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: fastqc_top_overrepresented_sequences_table

Sort	Visible	Group	Column	Description	ID	Scale

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

Created with MultiQC

Status Checks

Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

Min:

Max:

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Software	Version
FastQ Screen	`0.15.3`
FastQC	`0.12.1`

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QC

General Statistics

General Statistics: Columns

DRAGEN

Mapping metrics

Dragen-Mapping-Metrics-Table: Columns

Mapped / paired / duplicated

Variant calling

Dragen-Vc-Metrics-Table: Columns

Target Bed Coverage Metrics Help

Target Bed: Columns

WGS Coverage Metrics Help

WGS: Columns

Coverage distribution Help

Cumulative coverage hist Help

Coverage per contig

Coverage per contig (non-main)

Fragment length hist

Trimmer Metrics

Dragen-Trimmer-Metrics-Table: Columns

Time Metrics

DRAGEN-FastQC

Per-Position Mean Quality Scores Help

Per-Sequence Quality Scores Help

Sequence Length Distribution

Per-Sequence GC Content Help

GC Content Mean Quality Scores Help

Per-Position N Content Help

Per-Position Sequence Content Help

Rollover for sample name

Adapter Content Help

Picard

Alignment Summary

Mean read length

Base Distribution

GC Coverage Bias

Insert Size

Mark Duplicates Help

Mean Base Quality by Cycle Help

Base Quality Distribution

WGS Coverage

WGS Filtered Bases

FastQ Screen

Mapped Reads

FastQC

Sequence Counts Help

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Per Base N Content Help

Sequence Length Distribution

Sequence Duplication Levels Help

Overrepresented sequences by sample Help

Top overrepresented sequences

FastQC: Top overrepresented sequences: Columns

Adapter Content Help

Status Checks Help

Software Versions

v1.20

Highlight Samples

Rename Samples

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Target Bed Coverage Metrics

WGS Coverage Metrics

Coverage distribution

Cumulative coverage hist

Per-Position Mean Quality Scores

Per-Sequence Quality Scores

Per-Sequence GC Content

GC Content Mean Quality Scores

Per-Position N Content

Per-Position Sequence Content

Adapter Content

Mark Duplicates

Mean Base Quality by Cycle

Sequence Counts

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Per Base N Content

Sequence Duplication Levels

Overrepresented sequences by sample

Adapter Content

Status Checks